MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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List of Mg²⁺ binding sites in structure 3cc2

3CC2 (2.4Å) -- RIBOSOME : The refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution with rrna sequence for the 23s rrna and genome-derived sequences for r-proteins
List of all 116 Mg²⁺ binding sites in the PDB structure 3cc2 in the full dataset (switch to benchmark dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv ^#", "Qs ^#", "Qe ^#", "Site type" or "Mg²⁺ ID"
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Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
3cc2	08009	poly-nuclear Mg²⁺ site	6	0.94	0.90	0.86	yes
3cc2	08058	poly-nuclear Mg²⁺ site	6	0.90	0.90	0.91	yes
3cc2	08059	poly-nuclear Mg²⁺ site	6	0.60	0.90	0.90	yes
3cc2	08085	poly-nuclear Mg²⁺ site	6	0.31	0.85	0.73	no
3cc2	08114	poly-nuclear Mg²⁺ site	5	0.56	0.37	0.46	no
3cc2	08043	poly-nuclear Mg²⁺ site	5	0.34	0.79	0.97	no
3cc2	08057	poly-nuclear Mg²⁺ site	6	0.28	0.79	0.82	no
3cc2	08088	poly-nuclear Mg²⁺ site	6	0.29	0.92	0.91	no
3cc2	08096	poly-nuclear Mg²⁺ site	6	0.45	0.89	0.77	no
3cc2	08031	poly-nuclear Mg²⁺ site	6	0.98	0.96	0.97	yes
3cc2	08105	poly-nuclear Mg²⁺ site	6	0.38	0.79	0.74	no
3cc2	08079	poly-nuclear Mg²⁺ site	6	0.99	0.81	0.89	yes
3cc2	08115	poly-nuclear Mg²⁺ site	6	0.34	0.87	0.71	no
3cc2	08006	poly-nuclear Mg²⁺ site	6	0.90	0.91	0.91	yes
3cc2	Y8108	Mg²⁺ not bound by RNA	6	0.35	0.72	0.85	no
3cc2	T8073	Mg²⁺ not bound by RNA	6	0.29	0.66	0.50	no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Abbreviations used for Mg²⁺ "Site type"	Mg²⁺ inner-sphere ligands	Geometry for inner-sphere O_P	Mg²⁺ outer-sphere moieties
Site type used in the classification is a string abbreviation of ligand composition in Mg²⁺ coordination sphere
Abbreviations used for Mg²⁺ "Site type"	O_ph phosphate oxygen (OP1/OP2) O_r ribose oxygen (O2'/O4') or oxygen bridging phosphate and ribose (O3'/O5') O_b nucleobase oxygen N_b nucleobase nitrogen	*cis-* two O_P ligands adopt cis- isoform *trans-* two O_P ligands adopt trans- isoform *fac-* three O_P ligands adopt fac- isoform *mer-* three O_P ligands adopt mer- isoform	P_out phosphate moiety R_out ribose moiety B_out nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

List of Mg2+ binding sites in structure 3cc2

MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures

List of Mg²⁺ binding sites in structure 3cc2